To decontaminate is to clean something that's been poisoned or polluted. After last week's chemical spill, your chemist mom can't go back to the lab until they decontaminate the building.
When something is contaminated, it's made unsafe for humans (and other living things) due to some kind of poison or impurity. Workers have to decontaminate, or remove the contamination, after a disaster at a nuclear reactor produces radioactivity. An oil spill in the ocean requires a different type of decontamination. Hospital cleaners also have to decontaminate areas where patients with infectious diseases have been, scrubbing surfaces and filtering the air.